Starting phenix.real_space_refine on Mon Aug 25 14:54:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gjm_40094/08_2025/8gjm_40094_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gjm_40094/08_2025/8gjm_40094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gjm_40094/08_2025/8gjm_40094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gjm_40094/08_2025/8gjm_40094.map" model { file = "/net/cci-nas-00/data/ceres_data/8gjm_40094/08_2025/8gjm_40094_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gjm_40094/08_2025/8gjm_40094_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 18231 2.51 5 N 4653 2.21 5 O 5721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28728 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 8519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8519 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 52, 'TRANS': 1036} Chain breaks: 5 Chain: "B" Number of atoms: 8520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8520 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 5 Chain: "C" Number of atoms: 8605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8605 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 53, 'TRANS': 1045} Chain breaks: 4 Chain: "D" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.16, per 1000 atoms: 0.28 Number of scatterers: 28728 At special positions: 0 Unit cell: (150.975, 150.975, 250.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 5721 8.00 N 4653 7.00 C 18231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.18 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.92 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.37 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 108 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM28544 O5 NAG B1403 .*. O " rejected from bonding due to valence issues. Atom "HETATM28726 O5 NAG C1408 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG h 2 " - " MAN h 3 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " " NAG g 1 " - " FUC g 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 148 " " NAG A1403 " - " ASN A 234 " " NAG A1404 " - " ASN A 282 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1158 " " NAG A1409 " - " ASN A 165 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 148 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 148 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 616 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG F 1 " - " ASN A 17 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 343 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 282 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1074 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " " NAG Y 1 " - " ASN B 343 " " NAG Z 1 " - " ASN B 165 " " NAG a 1 " - " ASN C 17 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 717 " " NAG f 1 " - " ASN C 801 " " NAG g 1 " - " ASN C1074 " " NAG h 1 " - " ASN C1098 " " NAG i 1 " - " ASN C1134 " " NAG j 1 " - " ASN C 343 " " NAG k 1 " - " ASN C 165 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6550 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 48 sheets defined 25.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.106A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.074A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.910A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.670A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.778A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.149A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.898A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.560A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.151A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 3.956A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.539A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.562A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.385A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.694A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.622A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.640A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.786A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.085A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.411A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.016A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.989A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.263A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.172A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.660A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.908A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.908A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.292A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.884A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.934A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.032A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.719A pdb=" N TYR D 51 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 removed outlier: 4.450A pdb=" N GLY D 85 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.966A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.515A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 3.723A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.655A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.221A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 removed outlier: 3.626A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.877A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.851A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.460A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.154A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.557A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.520A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 3.794A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.175A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.627A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.806A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.072A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.010A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.330A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.780A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.477A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 31 current: chain 'C' and resid 78 through 79 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 3.738A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 11.322A pdb=" N SER C 221 " --> pdb=" O PRO C 209 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.522A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 120 removed outlier: 7.092A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.657A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 354 through 358 current: chain 'C' and resid 507 through 517 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.430A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.002A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.881A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.434A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE8, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.213A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 23 through 25 removed outlier: 6.071A pdb=" N ALA D 35 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER D 104 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 102 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 29 through 30 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 29 through 30 current: chain 'D' and resid 64 through 71 removed outlier: 3.853A pdb=" N SER D 76 " --> pdb=" O ASN D 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 76 through 79 current: chain 'D' and resid 124 through 128 Processing sheet with id=AF2, first strand: chain 'E' and resid 25 through 26 removed outlier: 4.157A pdb=" N VAL E 39 " --> pdb=" O ILE E 95 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 30 through 33 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 33 current: chain 'E' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 64 through 68 current: chain 'E' and resid 117 through 118 No H-bonds generated for sheet with id=AF3 1019 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.39 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4879 1.31 - 1.44: 8056 1.44 - 1.57: 16268 1.57 - 1.69: 1 1.69 - 1.82: 156 Bond restraints: 29360 Sorted by residual: bond pdb=" CA PRO A 527 " pdb=" C PRO A 527 " ideal model delta sigma weight residual 1.520 1.457 0.062 1.42e-02 4.96e+03 1.91e+01 bond pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.86e+01 bond pdb=" N LEU C 84 " pdb=" CA LEU C 84 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.67e+01 bond pdb=" CA ARG C 355 " pdb=" C ARG C 355 " ideal model delta sigma weight residual 1.522 1.568 -0.046 1.14e-02 7.69e+03 1.66e+01 bond pdb=" N ILE C 233 " pdb=" CA ILE C 233 " ideal model delta sigma weight residual 1.455 1.503 -0.048 1.18e-02 7.18e+03 1.65e+01 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 31621 2.10 - 4.19: 7678 4.19 - 6.29: 588 6.29 - 8.39: 32 8.39 - 10.49: 7 Bond angle restraints: 39926 Sorted by residual: angle pdb=" N ARG C1091 " pdb=" CA ARG C1091 " pdb=" C ARG C1091 " ideal model delta sigma weight residual 111.03 102.81 8.22 1.11e+00 8.12e-01 5.48e+01 angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.85 119.39 -7.54 1.06e+00 8.90e-01 5.06e+01 angle pdb=" N SER A 810 " pdb=" CA SER A 810 " pdb=" C SER A 810 " ideal model delta sigma weight residual 112.92 121.19 -8.27 1.23e+00 6.61e-01 4.52e+01 angle pdb=" N VAL B 213 " pdb=" CA VAL B 213 " pdb=" C VAL B 213 " ideal model delta sigma weight residual 110.42 116.32 -5.90 9.40e-01 1.13e+00 3.94e+01 angle pdb=" N ARG E 81 " pdb=" CA ARG E 81 " pdb=" C ARG E 81 " ideal model delta sigma weight residual 112.87 120.24 -7.37 1.20e+00 6.94e-01 3.77e+01 ... (remaining 39921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.27: 17791 24.27 - 48.54: 675 48.54 - 72.81: 188 72.81 - 97.08: 44 97.08 - 121.35: 32 Dihedral angle restraints: 18730 sinusoidal: 8541 harmonic: 10189 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -164.60 78.60 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -149.74 63.74 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -145.37 59.37 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 18727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4767 0.340 - 0.680: 15 0.680 - 1.020: 2 1.020 - 1.359: 1 1.359 - 1.699: 2 Chirality restraints: 4787 Sorted by residual: chirality pdb=" C1 MAN N 3 " pdb=" O4 NAG N 2 " pdb=" C2 MAN N 3 " pdb=" O5 MAN N 3 " both_signs ideal model delta sigma weight residual False 2.40 1.97 0.43 2.00e-02 2.50e+03 4.56e+02 chirality pdb=" C1 MAN X 3 " pdb=" O4 NAG X 2 " pdb=" C2 MAN X 3 " pdb=" O5 MAN X 3 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.29e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.71e+02 ... (remaining 4784 not shown) Planarity restraints: 5082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 2 " 0.345 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG d 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG d 2 " 0.155 2.00e-02 2.50e+03 pdb=" N2 NAG d 2 " -0.525 2.00e-02 2.50e+03 pdb=" O7 NAG d 2 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " -0.333 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG d 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1407 " -0.334 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG C1407 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C1407 " -0.172 2.00e-02 2.50e+03 pdb=" N2 NAG C1407 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG C1407 " -0.079 2.00e-02 2.50e+03 ... (remaining 5079 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 48 2.48 - 3.08: 19276 3.08 - 3.69: 43416 3.69 - 4.29: 66622 4.29 - 4.90: 107837 Nonbonded interactions: 237199 Sorted by model distance: nonbonded pdb=" OE1 GLN B 14 " pdb=" NH1 ARG B 158 " model vdw 1.875 3.120 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 1.965 3.120 nonbonded pdb=" NH1 ARG B 102 " pdb=" CD2 LEU B 179 " model vdw 2.144 2.832 nonbonded pdb=" NH1 ARG A 34 " pdb=" OE2 GLU A 191 " model vdw 2.144 3.120 nonbonded pdb=" O VAL B 620 " pdb=" NH2 ARG B 634 " model vdw 2.146 3.120 ... (remaining 237194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 68 or resid 77 through 826 or resid 854 through \ 1408)) selection = (chain 'B' and (resid 14 through 623 or resid 636 through 826 or resid 854 throu \ gh 1408)) selection = (chain 'C' and (resid 14 through 68 or resid 77 through 623 or resid 636 through \ 826 or resid 854 through 1408)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'k' } ncs_group { reference = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.910 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.310 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.406 29501 Z= 0.826 Angle : 1.767 39.957 40303 Z= 1.148 Chirality : 0.105 1.699 4787 Planarity : 0.020 0.296 5025 Dihedral : 14.978 121.354 12051 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.13 % Rotamer: Outliers : 0.95 % Allowed : 6.57 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.12), residues: 3463 helix: -1.84 (0.14), residues: 766 sheet: -0.18 (0.18), residues: 721 loop : -1.79 (0.12), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 509 TYR 0.119 0.016 TYR B 38 PHE 0.097 0.010 PHE A 718 TRP 0.169 0.018 TRP B 104 HIS 0.010 0.002 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.01237 (29360) covalent geometry : angle 1.67339 (39926) SS BOND : bond 0.06057 ( 43) SS BOND : angle 3.44695 ( 86) hydrogen bonds : bond 0.20605 ( 1019) hydrogen bonds : angle 9.20002 ( 2808) Misc. bond : bond 0.40553 ( 1) link_ALPHA1-4 : bond 0.00323 ( 5) link_ALPHA1-4 : angle 2.08335 ( 15) link_BETA1-4 : bond 0.00398 ( 32) link_BETA1-4 : angle 1.17125 ( 96) link_BETA1-6 : bond 0.01021 ( 3) link_BETA1-6 : angle 5.34590 ( 9) link_NAG-ASN : bond 0.01530 ( 57) link_NAG-ASN : angle 8.58298 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 304 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7801 (pp) REVERT: A 985 ASP cc_start: 0.7663 (p0) cc_final: 0.7446 (p0) REVERT: B 197 ILE cc_start: 0.8635 (mm) cc_final: 0.8257 (mp) REVERT: C 32 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7538 (p90) REVERT: C 226 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.5251 (mp) REVERT: C 574 ASP cc_start: 0.6583 (t0) cc_final: 0.6251 (t0) outliers start: 29 outliers final: 8 residues processed: 327 average time/residue: 0.6104 time to fit residues: 233.5860 Evaluate side-chains 121 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 74 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 149 ASN A 196 ASN A 360 ASN A 493 GLN A 540 ASN A 563 GLN A 606 ASN A 613 GLN A 853 GLN A 926 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 149 ASN B 207 HIS B 211 ASN B 448 ASN B 519 HIS B 658 ASN B 675 GLN B 804 GLN B 913 GLN B 926 GLN B 957 GLN B 969 ASN B 978 ASN C 121 ASN C 146 HIS C 314 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 110 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.104826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.064667 restraints weight = 85260.853| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.42 r_work: 0.3049 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29501 Z= 0.179 Angle : 0.783 14.372 40303 Z= 0.377 Chirality : 0.047 0.409 4787 Planarity : 0.005 0.056 5025 Dihedral : 9.953 102.931 5795 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.19 % Allowed : 10.00 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.13), residues: 3463 helix: 0.75 (0.18), residues: 746 sheet: -0.10 (0.18), residues: 774 loop : -1.19 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.020 0.002 TYR A 365 PHE 0.020 0.002 PHE B 456 TRP 0.018 0.001 TRP C 64 HIS 0.009 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00404 (29360) covalent geometry : angle 0.74289 (39926) SS BOND : bond 0.00367 ( 43) SS BOND : angle 1.43216 ( 86) hydrogen bonds : bond 0.04456 ( 1019) hydrogen bonds : angle 6.45613 ( 2808) Misc. bond : bond 0.00109 ( 1) link_ALPHA1-4 : bond 0.02039 ( 5) link_ALPHA1-4 : angle 2.58484 ( 15) link_BETA1-4 : bond 0.00486 ( 32) link_BETA1-4 : angle 1.46290 ( 96) link_BETA1-6 : bond 0.01415 ( 3) link_BETA1-6 : angle 2.26016 ( 9) link_NAG-ASN : bond 0.00546 ( 57) link_NAG-ASN : angle 3.56061 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 125 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7273 (ptt) cc_final: 0.6575 (pmm) REVERT: A 179 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7306 (pp) REVERT: A 619 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: A 776 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8316 (tptm) REVERT: A 1145 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7244 (pp) REVERT: B 24 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7968 (mp) REVERT: B 174 PRO cc_start: 0.9472 (Cg_exo) cc_final: 0.9268 (Cg_endo) REVERT: B 197 ILE cc_start: 0.9169 (mm) cc_final: 0.8965 (pp) REVERT: B 455 LEU cc_start: 0.8419 (tm) cc_final: 0.7940 (pp) REVERT: B 505 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: B 988 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8786 (tp30) REVERT: B 1010 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8584 (tm-30) REVERT: C 32 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7442 (p90) REVERT: C 226 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7144 (mp) REVERT: C 422 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8906 (p0) REVERT: C 988 GLU cc_start: 0.8381 (mp0) cc_final: 0.7924 (mp0) outliers start: 67 outliers final: 15 residues processed: 179 average time/residue: 0.5098 time to fit residues: 110.8711 Evaluate side-chains 117 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 57 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 2.9990 chunk 284 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 360 ASN A 935 GLN B 613 GLN B 856 ASN B 901 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 474 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.101358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057647 restraints weight = 82243.888| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 4.13 r_work: 0.2896 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29501 Z= 0.218 Angle : 0.694 11.948 40303 Z= 0.338 Chirality : 0.046 0.367 4787 Planarity : 0.004 0.048 5025 Dihedral : 7.635 100.720 5780 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.09 % Allowed : 11.07 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.14), residues: 3463 helix: 1.33 (0.19), residues: 749 sheet: -0.06 (0.18), residues: 772 loop : -1.06 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 408 TYR 0.031 0.002 TYR E 106 PHE 0.021 0.002 PHE C 565 TRP 0.022 0.001 TRP D 55 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00499 (29360) covalent geometry : angle 0.65774 (39926) SS BOND : bond 0.00911 ( 43) SS BOND : angle 1.60660 ( 86) hydrogen bonds : bond 0.04248 ( 1019) hydrogen bonds : angle 6.10898 ( 2808) Misc. bond : bond 0.00020 ( 1) link_ALPHA1-4 : bond 0.01652 ( 5) link_ALPHA1-4 : angle 2.63936 ( 15) link_BETA1-4 : bond 0.00344 ( 32) link_BETA1-4 : angle 1.32793 ( 96) link_BETA1-6 : bond 0.01424 ( 3) link_BETA1-6 : angle 2.24274 ( 9) link_NAG-ASN : bond 0.00413 ( 57) link_NAG-ASN : angle 3.03392 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 99 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7572 (ptt) cc_final: 0.6976 (pmm) REVERT: A 368 LEU cc_start: 0.9345 (mt) cc_final: 0.8975 (tp) REVERT: A 390 LEU cc_start: 0.9194 (mt) cc_final: 0.8908 (mp) REVERT: A 619 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8643 (mt-10) REVERT: A 994 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8243 (t0) REVERT: B 24 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7811 (mp) REVERT: B 455 LEU cc_start: 0.8419 (tm) cc_final: 0.7933 (pp) REVERT: B 505 TYR cc_start: 0.9103 (t80) cc_final: 0.8451 (t80) REVERT: C 32 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7495 (p90) REVERT: C 226 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7468 (mt) REVERT: C 408 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8457 (ppt90) REVERT: C 489 TYR cc_start: 0.8512 (m-80) cc_final: 0.8102 (m-80) REVERT: C 988 GLU cc_start: 0.8499 (mp0) cc_final: 0.7886 (mp0) REVERT: D 53 MET cc_start: 0.4485 (mmm) cc_final: 0.3830 (tmt) outliers start: 64 outliers final: 18 residues processed: 156 average time/residue: 0.4953 time to fit residues: 95.0214 Evaluate side-chains 101 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 856 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 336 optimal weight: 0.7980 chunk 264 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 327 optimal weight: 30.0000 chunk 199 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A1002 GLN A1142 GLN B1010 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 519 HIS C1005 GLN ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.101185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056999 restraints weight = 81609.124| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.28 r_work: 0.2889 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29501 Z= 0.172 Angle : 0.636 17.059 40303 Z= 0.304 Chirality : 0.044 0.361 4787 Planarity : 0.004 0.077 5025 Dihedral : 6.766 93.936 5778 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.89 % Allowed : 11.79 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.14), residues: 3463 helix: 1.69 (0.19), residues: 746 sheet: -0.14 (0.17), residues: 796 loop : -0.94 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 214 TYR 0.021 0.001 TYR C 453 PHE 0.013 0.001 PHE A 898 TRP 0.007 0.001 TRP C 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00391 (29360) covalent geometry : angle 0.60671 (39926) SS BOND : bond 0.00340 ( 43) SS BOND : angle 1.16121 ( 86) hydrogen bonds : bond 0.03640 ( 1019) hydrogen bonds : angle 5.86063 ( 2808) Misc. bond : bond 0.00007 ( 1) link_ALPHA1-4 : bond 0.01878 ( 5) link_ALPHA1-4 : angle 2.58721 ( 15) link_BETA1-4 : bond 0.00382 ( 32) link_BETA1-4 : angle 1.23944 ( 96) link_BETA1-6 : bond 0.01695 ( 3) link_BETA1-6 : angle 2.51026 ( 9) link_NAG-ASN : bond 0.00375 ( 57) link_NAG-ASN : angle 2.66012 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 96 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8406 (t60) cc_final: 0.8097 (t60) REVERT: A 177 MET cc_start: 0.7786 (ptt) cc_final: 0.7372 (pmm) REVERT: A 179 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7596 (pp) REVERT: A 309 GLU cc_start: 0.8493 (pm20) cc_final: 0.8204 (pm20) REVERT: A 390 LEU cc_start: 0.9270 (mt) cc_final: 0.9012 (mp) REVERT: A 619 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8649 (mt-10) REVERT: B 24 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7848 (mp) REVERT: B 455 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7964 (pp) REVERT: B 986 LYS cc_start: 0.9303 (tppp) cc_final: 0.8715 (tptt) REVERT: C 32 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7474 (p90) REVERT: C 226 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7637 (mt) REVERT: C 360 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8981 (t0) REVERT: C 422 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8847 (p0) REVERT: C 489 TYR cc_start: 0.8512 (m-80) cc_final: 0.8276 (m-80) REVERT: C 988 GLU cc_start: 0.8767 (mp0) cc_final: 0.8247 (mp0) REVERT: D 53 MET cc_start: 0.4415 (mmm) cc_final: 0.3527 (tmt) outliers start: 58 outliers final: 23 residues processed: 148 average time/residue: 0.5807 time to fit residues: 103.2848 Evaluate side-chains 114 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 336 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 327 optimal weight: 50.0000 chunk 236 optimal weight: 0.3980 chunk 164 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 320 optimal weight: 0.8980 chunk 305 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN B 957 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 149 ASN ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.100820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059484 restraints weight = 81617.101| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.96 r_work: 0.2875 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29501 Z= 0.156 Angle : 0.608 11.652 40303 Z= 0.291 Chirality : 0.043 0.347 4787 Planarity : 0.004 0.049 5025 Dihedral : 6.255 92.253 5778 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 2.06 % Allowed : 12.09 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.14), residues: 3463 helix: 1.86 (0.19), residues: 740 sheet: -0.15 (0.17), residues: 796 loop : -0.90 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.020 0.001 TYR C1067 PHE 0.014 0.001 PHE C 898 TRP 0.006 0.001 TRP C 64 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00355 (29360) covalent geometry : angle 0.57948 (39926) SS BOND : bond 0.00239 ( 43) SS BOND : angle 1.06643 ( 86) hydrogen bonds : bond 0.03560 ( 1019) hydrogen bonds : angle 5.72901 ( 2808) Misc. bond : bond 0.00001 ( 1) link_ALPHA1-4 : bond 0.01571 ( 5) link_ALPHA1-4 : angle 2.54604 ( 15) link_BETA1-4 : bond 0.00356 ( 32) link_BETA1-4 : angle 1.19460 ( 96) link_BETA1-6 : bond 0.01579 ( 3) link_BETA1-6 : angle 2.38054 ( 9) link_NAG-ASN : bond 0.00349 ( 57) link_NAG-ASN : angle 2.53502 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 90 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7563 (ptt) cc_final: 0.7319 (pmm) REVERT: A 179 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7610 (pp) REVERT: A 309 GLU cc_start: 0.8532 (pm20) cc_final: 0.8272 (pm20) REVERT: A 390 LEU cc_start: 0.9364 (mt) cc_final: 0.9136 (mp) REVERT: A 619 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8643 (mt-10) REVERT: A 994 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8285 (t0) REVERT: B 24 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7855 (mp) REVERT: B 455 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8023 (pp) REVERT: B 759 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8056 (OUTLIER) REVERT: B 986 LYS cc_start: 0.9320 (tppp) cc_final: 0.8801 (tptt) REVERT: C 32 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7527 (p90) REVERT: C 177 MET cc_start: 0.6045 (ptm) cc_final: 0.5271 (pmm) REVERT: C 360 ASN cc_start: 0.9258 (OUTLIER) cc_final: 0.8981 (t0) REVERT: C 408 ARG cc_start: 0.8796 (ttp80) cc_final: 0.8317 (ppt90) REVERT: C 489 TYR cc_start: 0.8650 (m-80) cc_final: 0.8340 (m-80) REVERT: C 988 GLU cc_start: 0.8818 (mp0) cc_final: 0.8300 (mp0) REVERT: D 53 MET cc_start: 0.4374 (mmm) cc_final: 0.3874 (tmt) outliers start: 63 outliers final: 31 residues processed: 145 average time/residue: 0.5706 time to fit residues: 101.1825 Evaluate side-chains 114 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 241 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 199 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 182 optimal weight: 0.4980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 762 GLN B 957 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.099908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.058397 restraints weight = 81427.182| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.08 r_work: 0.2834 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 29501 Z= 0.203 Angle : 0.618 9.939 40303 Z= 0.296 Chirality : 0.043 0.349 4787 Planarity : 0.004 0.049 5025 Dihedral : 5.868 89.231 5776 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 2.19 % Allowed : 12.15 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.14), residues: 3463 helix: 1.93 (0.19), residues: 734 sheet: -0.26 (0.17), residues: 793 loop : -0.89 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.021 0.001 TYR C1067 PHE 0.026 0.001 PHE C 456 TRP 0.010 0.001 TRP B 64 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00466 (29360) covalent geometry : angle 0.58985 (39926) SS BOND : bond 0.00307 ( 43) SS BOND : angle 1.09255 ( 86) hydrogen bonds : bond 0.03667 ( 1019) hydrogen bonds : angle 5.73752 ( 2808) Misc. bond : bond 0.00008 ( 1) link_ALPHA1-4 : bond 0.01935 ( 5) link_ALPHA1-4 : angle 3.00817 ( 15) link_BETA1-4 : bond 0.00317 ( 32) link_BETA1-4 : angle 1.22382 ( 96) link_BETA1-6 : bond 0.01701 ( 3) link_BETA1-6 : angle 2.55094 ( 9) link_NAG-ASN : bond 0.00368 ( 57) link_NAG-ASN : angle 2.50072 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 88 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7978 (ptt) cc_final: 0.7527 (pmm) REVERT: A 214 ARG cc_start: 0.7673 (tpm170) cc_final: 0.7443 (tpm170) REVERT: A 309 GLU cc_start: 0.8583 (pm20) cc_final: 0.8323 (pm20) REVERT: A 619 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: A 745 ASP cc_start: 0.7293 (m-30) cc_final: 0.6789 (p0) REVERT: A 994 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8338 (t0) REVERT: B 455 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7981 (pp) REVERT: B 986 LYS cc_start: 0.9316 (tppp) cc_final: 0.8823 (tptt) REVERT: C 32 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7457 (p90) REVERT: C 177 MET cc_start: 0.6210 (ptm) cc_final: 0.5350 (pmm) REVERT: C 408 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8371 (ppt90) REVERT: C 489 TYR cc_start: 0.8661 (m-80) cc_final: 0.8459 (m-80) REVERT: C 988 GLU cc_start: 0.9003 (mp0) cc_final: 0.8556 (mp0) REVERT: D 53 MET cc_start: 0.4498 (mmm) cc_final: 0.3868 (tmt) outliers start: 67 outliers final: 28 residues processed: 150 average time/residue: 0.5925 time to fit residues: 108.1375 Evaluate side-chains 113 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 138 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 chunk 258 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 762 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.099643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055570 restraints weight = 81159.449| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.39 r_work: 0.2828 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29501 Z= 0.197 Angle : 0.612 11.692 40303 Z= 0.291 Chirality : 0.043 0.337 4787 Planarity : 0.003 0.050 5025 Dihedral : 5.440 81.516 5776 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 1.83 % Allowed : 13.03 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.14), residues: 3463 helix: 1.93 (0.19), residues: 738 sheet: -0.33 (0.17), residues: 785 loop : -0.82 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 408 TYR 0.021 0.001 TYR C1067 PHE 0.016 0.001 PHE B1148 TRP 0.009 0.001 TRP B 64 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00450 (29360) covalent geometry : angle 0.58619 (39926) SS BOND : bond 0.00278 ( 43) SS BOND : angle 0.97384 ( 86) hydrogen bonds : bond 0.03610 ( 1019) hydrogen bonds : angle 5.70892 ( 2808) Misc. bond : bond 0.00017 ( 1) link_ALPHA1-4 : bond 0.02007 ( 5) link_ALPHA1-4 : angle 3.19479 ( 15) link_BETA1-4 : bond 0.00320 ( 32) link_BETA1-4 : angle 1.16316 ( 96) link_BETA1-6 : bond 0.01760 ( 3) link_BETA1-6 : angle 2.45823 ( 9) link_NAG-ASN : bond 0.00345 ( 57) link_NAG-ASN : angle 2.38396 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 87 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7886 (ptt) cc_final: 0.7639 (pmm) REVERT: A 309 GLU cc_start: 0.8532 (pm20) cc_final: 0.8246 (pm20) REVERT: A 368 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8904 (tp) REVERT: A 619 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8672 (mt-10) REVERT: A 987 VAL cc_start: 0.9032 (t) cc_final: 0.8654 (p) REVERT: A 988 GLU cc_start: 0.8929 (pt0) cc_final: 0.8466 (pm20) REVERT: A 994 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8307 (t0) REVERT: B 455 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7906 (pp) REVERT: B 986 LYS cc_start: 0.9263 (tppp) cc_final: 0.8809 (tptt) REVERT: C 32 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7187 (p90) REVERT: C 177 MET cc_start: 0.6294 (ptm) cc_final: 0.5343 (pmm) REVERT: C 408 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8300 (ppt90) REVERT: C 489 TYR cc_start: 0.8705 (m-80) cc_final: 0.8493 (m-80) REVERT: C 988 GLU cc_start: 0.9026 (mp0) cc_final: 0.8537 (mp0) REVERT: C 1002 GLN cc_start: 0.9121 (tp40) cc_final: 0.8887 (tp40) REVERT: D 53 MET cc_start: 0.4511 (mmm) cc_final: 0.3689 (tmt) outliers start: 56 outliers final: 33 residues processed: 138 average time/residue: 0.6055 time to fit residues: 101.6842 Evaluate side-chains 118 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 281 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 280 optimal weight: 0.6980 chunk 188 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.100094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.056407 restraints weight = 81093.118| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.23 r_work: 0.2855 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29501 Z= 0.138 Angle : 0.584 10.998 40303 Z= 0.277 Chirality : 0.042 0.337 4787 Planarity : 0.003 0.050 5025 Dihedral : 5.147 70.789 5776 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.83 % Allowed : 13.10 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.14), residues: 3463 helix: 2.00 (0.19), residues: 739 sheet: -0.31 (0.17), residues: 783 loop : -0.75 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.020 0.001 TYR C1067 PHE 0.027 0.001 PHE C 456 TRP 0.007 0.001 TRP C 258 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00309 (29360) covalent geometry : angle 0.55881 (39926) SS BOND : bond 0.00255 ( 43) SS BOND : angle 0.91099 ( 86) hydrogen bonds : bond 0.03415 ( 1019) hydrogen bonds : angle 5.63564 ( 2808) Misc. bond : bond 0.00011 ( 1) link_ALPHA1-4 : bond 0.01967 ( 5) link_ALPHA1-4 : angle 3.17524 ( 15) link_BETA1-4 : bond 0.00340 ( 32) link_BETA1-4 : angle 1.13550 ( 96) link_BETA1-6 : bond 0.01902 ( 3) link_BETA1-6 : angle 2.49112 ( 9) link_NAG-ASN : bond 0.00335 ( 57) link_NAG-ASN : angle 2.29033 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 84 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7837 (ptt) cc_final: 0.7378 (pmm) REVERT: A 214 ARG cc_start: 0.7686 (tpm170) cc_final: 0.7339 (tpm170) REVERT: A 309 GLU cc_start: 0.8494 (pm20) cc_final: 0.8218 (pm20) REVERT: A 368 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8839 (tp) REVERT: A 740 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8906 (ttp) REVERT: A 987 VAL cc_start: 0.9027 (t) cc_final: 0.8656 (p) REVERT: A 988 GLU cc_start: 0.8952 (pt0) cc_final: 0.8491 (pm20) REVERT: A 994 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8315 (t0) REVERT: B 455 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7918 (pp) REVERT: B 986 LYS cc_start: 0.9268 (tppp) cc_final: 0.8792 (tptt) REVERT: C 115 GLN cc_start: 0.9146 (mt0) cc_final: 0.8538 (mm-40) REVERT: C 177 MET cc_start: 0.6255 (ptm) cc_final: 0.5315 (pmm) REVERT: C 360 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8922 (t0) REVERT: C 408 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8300 (ppt90) REVERT: C 489 TYR cc_start: 0.8754 (m-80) cc_final: 0.8543 (m-80) REVERT: C 988 GLU cc_start: 0.9029 (mp0) cc_final: 0.8584 (mp0) REVERT: C 1002 GLN cc_start: 0.9097 (tp40) cc_final: 0.8853 (tp40) REVERT: D 53 MET cc_start: 0.4442 (mmm) cc_final: 0.3646 (tmt) outliers start: 56 outliers final: 36 residues processed: 133 average time/residue: 0.5492 time to fit residues: 88.8707 Evaluate side-chains 118 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 18 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 261 optimal weight: 0.0170 chunk 181 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.100171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.059446 restraints weight = 80464.113| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.81 r_work: 0.2835 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29501 Z= 0.161 Angle : 0.588 9.523 40303 Z= 0.279 Chirality : 0.042 0.329 4787 Planarity : 0.003 0.050 5025 Dihedral : 4.847 58.419 5776 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 13.10 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.14), residues: 3463 helix: 2.09 (0.19), residues: 732 sheet: -0.29 (0.17), residues: 787 loop : -0.73 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.019 0.001 TYR C1067 PHE 0.014 0.001 PHE C 898 TRP 0.008 0.001 TRP C 258 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00366 (29360) covalent geometry : angle 0.56332 (39926) SS BOND : bond 0.00247 ( 43) SS BOND : angle 0.89994 ( 86) hydrogen bonds : bond 0.03460 ( 1019) hydrogen bonds : angle 5.58299 ( 2808) Misc. bond : bond 0.00024 ( 1) link_ALPHA1-4 : bond 0.01912 ( 5) link_ALPHA1-4 : angle 3.20056 ( 15) link_BETA1-4 : bond 0.00308 ( 32) link_BETA1-4 : angle 1.14387 ( 96) link_BETA1-6 : bond 0.01910 ( 3) link_BETA1-6 : angle 2.28837 ( 9) link_NAG-ASN : bond 0.00326 ( 57) link_NAG-ASN : angle 2.25963 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 82 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8537 (pm20) cc_final: 0.8241 (pm20) REVERT: A 368 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8961 (tp) REVERT: A 987 VAL cc_start: 0.9067 (t) cc_final: 0.8680 (p) REVERT: A 988 GLU cc_start: 0.8985 (pt0) cc_final: 0.8492 (pm20) REVERT: A 994 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8289 (t0) REVERT: B 455 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.7982 (pp) REVERT: B 565 PHE cc_start: 0.7886 (m-80) cc_final: 0.7651 (m-80) REVERT: B 986 LYS cc_start: 0.9231 (tppp) cc_final: 0.8740 (tptt) REVERT: C 115 GLN cc_start: 0.9101 (mt0) cc_final: 0.8484 (mm-40) REVERT: C 177 MET cc_start: 0.6363 (ptm) cc_final: 0.5395 (pmm) REVERT: C 360 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8895 (t0) REVERT: C 408 ARG cc_start: 0.8790 (ttp80) cc_final: 0.8348 (ppt90) REVERT: C 988 GLU cc_start: 0.9075 (mp0) cc_final: 0.8615 (mp0) REVERT: C 1002 GLN cc_start: 0.9112 (tp40) cc_final: 0.8877 (tp40) REVERT: C 1141 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8943 (tm) REVERT: D 53 MET cc_start: 0.4312 (mmm) cc_final: 0.3850 (tmt) outliers start: 58 outliers final: 33 residues processed: 134 average time/residue: 0.5317 time to fit residues: 87.5525 Evaluate side-chains 116 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 77 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 97 optimal weight: 0.0570 chunk 260 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 324 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 474 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.100541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056465 restraints weight = 80165.407| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.23 r_work: 0.2860 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29501 Z= 0.135 Angle : 0.589 11.392 40303 Z= 0.279 Chirality : 0.042 0.307 4787 Planarity : 0.003 0.050 5025 Dihedral : 4.733 58.582 5776 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 1.34 % Allowed : 13.95 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.14), residues: 3463 helix: 2.13 (0.19), residues: 732 sheet: -0.28 (0.17), residues: 788 loop : -0.72 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.019 0.001 TYR C1067 PHE 0.055 0.001 PHE C 456 TRP 0.008 0.001 TRP C 258 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00306 (29360) covalent geometry : angle 0.56574 (39926) SS BOND : bond 0.00241 ( 43) SS BOND : angle 0.92397 ( 86) hydrogen bonds : bond 0.03371 ( 1019) hydrogen bonds : angle 5.52317 ( 2808) Misc. bond : bond 0.00011 ( 1) link_ALPHA1-4 : bond 0.01889 ( 5) link_ALPHA1-4 : angle 3.12691 ( 15) link_BETA1-4 : bond 0.00338 ( 32) link_BETA1-4 : angle 1.10252 ( 96) link_BETA1-6 : bond 0.01912 ( 3) link_BETA1-6 : angle 2.18952 ( 9) link_NAG-ASN : bond 0.00312 ( 57) link_NAG-ASN : angle 2.17618 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7982 (pmm) cc_final: 0.7768 (pmm) REVERT: A 309 GLU cc_start: 0.8517 (pm20) cc_final: 0.8238 (pm20) REVERT: A 368 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8943 (tp) REVERT: A 987 VAL cc_start: 0.9071 (t) cc_final: 0.8652 (p) REVERT: A 988 GLU cc_start: 0.8989 (pt0) cc_final: 0.8507 (pm20) REVERT: A 994 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8296 (t0) REVERT: B 455 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7925 (pp) REVERT: B 565 PHE cc_start: 0.7917 (m-80) cc_final: 0.7662 (m-80) REVERT: B 986 LYS cc_start: 0.9257 (tppp) cc_final: 0.8853 (tptt) REVERT: C 115 GLN cc_start: 0.9152 (mt0) cc_final: 0.8574 (mm-40) REVERT: C 177 MET cc_start: 0.6291 (ptm) cc_final: 0.5336 (pmm) REVERT: C 360 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8898 (t0) REVERT: C 547 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7761 (p) REVERT: C 988 GLU cc_start: 0.9027 (mp0) cc_final: 0.8588 (mp0) REVERT: C 1002 GLN cc_start: 0.9110 (tp40) cc_final: 0.8885 (tp40) REVERT: D 53 MET cc_start: 0.4273 (mmm) cc_final: 0.3435 (tmt) REVERT: D 70 ILE cc_start: 0.6395 (OUTLIER) cc_final: 0.5712 (mp) outliers start: 41 outliers final: 31 residues processed: 120 average time/residue: 0.5713 time to fit residues: 83.1136 Evaluate side-chains 116 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 244 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 305 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 314 optimal weight: 0.0970 chunk 293 optimal weight: 0.7980 chunk 268 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 274 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.100694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.058052 restraints weight = 80629.213| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.14 r_work: 0.2886 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29501 Z= 0.115 Angle : 0.567 9.544 40303 Z= 0.269 Chirality : 0.042 0.321 4787 Planarity : 0.003 0.050 5025 Dihedral : 4.533 58.685 5776 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 1.54 % Allowed : 13.79 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.14), residues: 3463 helix: 2.22 (0.19), residues: 727 sheet: -0.22 (0.18), residues: 798 loop : -0.68 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 457 TYR 0.018 0.001 TYR C1067 PHE 0.014 0.001 PHE A 855 TRP 0.009 0.001 TRP C 258 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00257 (29360) covalent geometry : angle 0.54406 (39926) SS BOND : bond 0.00219 ( 43) SS BOND : angle 0.89645 ( 86) hydrogen bonds : bond 0.03223 ( 1019) hydrogen bonds : angle 5.41063 ( 2808) Misc. bond : bond 0.00000 ( 1) link_ALPHA1-4 : bond 0.01823 ( 5) link_ALPHA1-4 : angle 3.08219 ( 15) link_BETA1-4 : bond 0.00352 ( 32) link_BETA1-4 : angle 1.08304 ( 96) link_BETA1-6 : bond 0.01872 ( 3) link_BETA1-6 : angle 2.18506 ( 9) link_NAG-ASN : bond 0.00317 ( 57) link_NAG-ASN : angle 2.12010 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11965.42 seconds wall clock time: 204 minutes 21.45 seconds (12261.45 seconds total)